RetrogeneDB ID: retro_hvul_11

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:559209383..559209929(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_66583
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_67451
• Aliases: None
• Description: None

Sequence

>retro_hvul_11
ATGGCGGGCGTCGGTCGCAACATGGTGGCGCCGTTGCTGGTGCTGAACCTCATCATGTACATCATCGTCATCGGGTTCGC
GAGCTGGAACCTCAACCACTTCATCAACGGCATCACCAACCGCCCCGGCGTAGGCGGCAACGGCGCCACCTTCTACTTCC
TCGTCTTCGCCATCCTTGCCGGGGTCGTCGGCGCGGCATCCAAGCTCGCCGGAGTGCACCACGTCCGTACCTGGCGTGGG
GACAGCCTCGCCACCTCCGCCTCTTCTTCGCTGGTGGCCTGGGCGATTACCGCCTTGGCCTTCGGGCTGGCGTGCAAGGA
GATCCACGTCGGCGGGTACCGGGGGTGGCGCCTCAGGGTGCTGGAGGCGTTCGTCATCATCCTCGCCTTCACGCAGCTCC
TGTACGTGCTTGCTCTCCACTCTGGGCTCTTCGGAAACCAGTTTGGTAATAACAATGGTGGGTATCCGGCGGAGCACGCT
TACGGCGCCGGCGTCGGTGACCACCACAACAAGGGCATGGACACCGGCGGCGTCGCAAGGGTCTAA

Alignment

ORF - retro_hvul_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.33 %
• Parental protein coverage: 78.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGAASRRYIGPLLCINLVMHAAVLGISGWSLNKFIDRETHRH-LGGNTATGYLLVFSLMAGVVGACSVLP
          .....R....PLL..NL.M...V.G...W.LN.FI...T.R...GGN.AT.Y.LVF...AGVVGA.S.L.
Retrocopy MAGVGRNMVAPLLVLNLIMYIIVIGFASWNLNHFINGITNRPGVGGNGATFYFLVFAILAGVVGAASKLA

Parental  ALLHVRAPWHSESLAAAASTGLVSWALTALAFGLACKHITLGN-RGRRLRTLEAFITISTLTQLFYLLLL
          ...HVR..W...SLA..AS..LV.WA.TALAFGLACK.I..G..RG.RLR.LEAF..I...TQL.Y.L.L
Retrocopy GVHHVRT-WRGDSLATSASSSLVAWAITALAFGLACKEIHVGGYRGWRLRVLEAFVIILAFTQLLYVLAL

Parental  HAGALSGVLG
          H.G......G
Retrocopy HSGLFGNQFG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Hordeum vulgare was not studied using RNA-Seq expression data.

ChIP-Seq

Hordeum vulgare was not studied using ChIP-Seq data.

EST

Hordeum vulgare was not studied using EST data.

TSS

Hordeum vulgare was not studied using FANTOM5 data.

Lab

retro_hvul_11 was not experimentally validated.

Homology

Retrocopy orthology:

Hordeum vulgare does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_67451	1 retrocopy	retro_hvul_11 ,
Oryza rufipogon	ORUFI02G33000	1 retrocopy	retro_oruf_20,